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Forensic DNA

Verica Radojicic, Milica Keckarevic Markovic, Feđa Puac, Miljana Kecmanovic, Dusan Keckarevic
Casings represent common evidence in a forensic laboratory, due to high frequency of firearms usage during perpetration of criminal offenses. Possible DNA evidence from casings is compromised by degradation, inhibition, and initial low-quantity deposition of biological material. For that reason, in the last 15 years, scientists have been trying to optimize procedures for recovery and amplification of DNA possibly present on its surface. In this study, we share our 12-year experience done on a total of 698 casework casings, comparing two DNA recovery methods commonly used-soaking and swabbing, as well as efficacy of two commercially available DNA amplification kits (AmpFLSTR® Identifiler® and AmpFLSTR® Identifiler® Plus kits)...
March 13, 2018: International Journal of Legal Medicine
Concetta Federico, Debora Lombardo, Noemi La Porta, Anna Maria Pappalardo, Venera Ferrito, Francesco Lombardo, Salvatore Saccone
The arrival of arthropods at a corpse exhibits specific temporal patterns, and Diptera play a key role in the initial stages of the decomposition process. Thus, the correct species assignment of the insect larvae found on a decomposing body is an important step in forensic investigations. Here, we describe a molecular procedure to define the species at larval age found on a corpse more quickly and easily than current systems. Our method involves a unique PCR amplification of a DNA segment within the evolutionarily conserved wingless gene, involved in embryo development...
March 6, 2018: Journal of Forensic and Legal Medicine
Nathan Scudder, Dennis McNevin, Sally F Kelty, Simon J Walsh, James Robertson
Use of DNA in forensic science will be significantly influenced by new technology in coming years. Massively parallel sequencing and forensic genomics will hasten the broadening of forensic DNA analysis beyond short tandem repeats for identity towards a wider array of genetic markers, in applications as diverse as predictive phenotyping, ancestry assignment, and full mitochondrial genome analysis. With these new applications come a range of legal and policy implications, as forensic science touches on areas as diverse as 'big data', privacy and protected health information...
March 2018: Science & Justice: Journal of the Forensic Science Society
Patricia P Albani, Rachel Fleming
In forensic investigations, the identification of the cellular or body fluid source of biological evidence can provide crucial probative information for the court. Messenger RNA (mRNA) profiling has become a valuable tool for body fluid and cell type identification due to its high sensitivity and compatibility with DNA analysis. However, using a single marker to determine the somatic origin of a sample can lead to misinterpretation as a result of cross-reactions. While false positives may be avoided through the simultaneous detection of multiple markers per body fluid, this approach is currently limited by the small number of known differentially expressed mRNAs...
March 2018: Science & Justice: Journal of the Forensic Science Society
Rebecca S Just, Jodi A Irwin
Some of the expected advantages of next generation sequencing (NGS) for short tandem repeat (STR) typing include enhanced mixture detection and genotype resolution via sequence variation among non-homologous alleles of the same length. However, at the same time that NGS methods for forensic DNA typing have advanced in recent years, many caseworking laboratories have implemented or are transitioning to probabilistic genotyping to assist the interpretation of complex autosomal STR typing results. Current probabilistic software programs are designed for length-based data, and were not intended to accommodate sequence strings as the product input...
February 21, 2018: Forensic Science International. Genetics
Nikhil Bose, Katie Carlberg, George Sensabaugh, Henry Erlich, Cassandra Calloway
DNA from biological forensic samples can be highly fragmented and present in limited quantity. When DNA is highly fragmented, conventional PCR based Short Tandem Repeat (STR) analysis may fail as primer binding sites may not be present on a single template molecule. Single Nucleotide Polymorphisms (SNPs) can serve as an alternative type of genetic marker for analysis of degraded samples because the targeted variation is a single base. However, conventional PCR based SNP analysis methods still require intact primer binding sites for target amplification...
February 4, 2018: Forensic Science International. Genetics
Jack Morrison, Giles Watts, Glyn Hobbs, Nick Dawnay
Field based forensic tests commonly provide information on the presence and identity of biological stains and can also support the identification of species. Such information can support downstream processing of forensic samples and generate rapid intelligence. These approaches have traditionally used chemical and immunological techniques to elicit the result but some are known to suffer from a lack of specificity and sensitivity. The last 10 years has seen the development of field-based genetic profiling systems, with specific focus on moving the mainstay of forensic genetic analysis, namely STR profiling, out of the laboratory and into the hands of the non-laboratory user...
February 21, 2018: Forensic Science International
Maja Sidstedt, Johannes Hedman, Erica L Romsos, Leticia Waitara, Lars Wadsö, Carolyn R Steffen, Peter M Vallone, Peter Rådström
Blood samples are widely used for PCR-based DNA analysis in fields such as diagnosis of infectious diseases, cancer diagnostics, and forensic genetics. In this study, the mechanisms behind blood-induced PCR inhibition were evaluated by use of whole blood as well as known PCR-inhibitory molecules in both digital PCR and real-time PCR. Also, electrophoretic mobility shift assay was applied to investigate interactions between inhibitory proteins and DNA, and isothermal titration calorimetry was used to directly measure effects on DNA polymerase activity...
March 5, 2018: Analytical and Bioanalytical Chemistry
Atif Adnan, Xiaoni Zhan, Kadirya Kasim, Allah Rakha, Xing Jia Xin
Forensic statistical parameters based on allelic frequencies of commonly used short tandem repeats were estimated for the Han population of Jiangsu province from P.R. China. The 6-dye GlobalFiler™ PCR amplification kit incorporates 21 autosomal STRs, providing reliable DNA typing results with enhanced the power of discrimination. Here, we analyzed the GlobalFiler™ STR loci in 516 unrelated individuals from Jiangsu Han population. A total of 256 alleles were observed ranging between 5 and 35.2 repeat units, and SE33 showed the greatest power of discrimination (34 alleles) in Jiangsu Han population...
March 2, 2018: International Journal of Legal Medicine
Lan Yao, Zhen Xu, Hemiao Zhao, Zheng Tu, Zhifang Liu, Wanshui Li, Lan Hu, Lihua Wan
In this study, the complete mitochondrial genome (mtGenome) of six samples from three forensic cases was sequenced using the Ion Torrent Personal Genome Machine (PGM). The analyzed samples from forensic cases included bloodstains from several materials, such as gauze, Flinder's Technology Associates (FTA) cards and swabs. The age of the samples ranged from two months to twelve years. The complete mtGenomes were amplified using the tiling sequencing strategy which divided the whole mtGenome into 162 amplicons...
February 27, 2018: Legal Medicine
Mahnaz Sheikhi, Mohammad Zandi, Maryam Ghazizadeh
Background: Palatal rugoscopy is a reliable method in the forensic personal identification and racial group specification. the aim of the present study is to use palatal rugae pattern in sex and ethnicity identification applications. Materials and Methods: Four hundred individual dental casts from four different ethnic populations of Iran were randomly selected. The pattern of the palatal rugae (shape, length, and number) investigated and its reliability to classify sex and minor ethnicity for each individual cast was evaluated...
January 2018: Dental Research Journal
Mitchell M Holland, Kateryna D Makova, Jennifer A McElhoe
Abstract : Distinguishing between maternal relatives through mitochondrial (mt) DNA sequence analysis has been a longstanding desire of the forensic community. Using a deep-coverage, massively parallel sequencing (DCMPS) approach, we studied the pattern of mtDNA heteroplasmy across the mtgenomes of 39 mother-child pairs of European decent; haplogroups H, J, K, R, T, U, and X. Both shared and differentiating heteroplasmy were observed on a frequent basis in these closely related maternal relatives, with the minor variant often presented as 2-10% of the sequencing reads...
February 26, 2018: Genes
Mark D Timken, Sonja B Klein, Martin R Buoncristiani
The efficacy of a DNA differential extraction procedure relies on reducing the amount of non-sperm female DNA carryover into the sperm fraction, while providing a sufficient recovery of male DNA from the sperm cell component. A standard approach to this extraction is to use a mild initial lysis step to digest the female (epithelial cell) component in the mixture, followed by a series of centrifugation and wash steps to further purify the resulting sperm-pellet fraction. This sperm fraction is then digested in the presence of a chemical reducing agent in preparation for DNA extraction...
February 21, 2018: Forensic Science International. Genetics
Le Wang, Man Chen, Bo Wu, Yi-Cheng Liu, Guang-Feng Zhang, Li Jiang, Xiu-Lan Xu, Xing-Chun Zhao, An-Quan Ji, Jian Ye
Next-generation sequencing (NGS) has been used to genotype forensic short tandem repeat (STR) markers for individual identification and kinship analysis. STR data from several NGS platforms have been published, but forensic application trials using the Ion S5™ XL system have not been reported. In this work, we report sensitivity, reproducibility, mixture, simulated degradation, and casework sample data on the Ion Chef™ and S5™ XL systems using an early access 25-plex panel. Sensitivity experiments showed that over 97% of the alleles were detectable with down to 62 pg input of genomic DNA...
March 1, 2018: Journal of Forensic Sciences
Odile Loreille, Shashikala Ratnayake, Adam L Bazinet, Timothy B Stockwell, Daniel D Sommer, Nadin Rohland, Swapan Mallick, Philip L F Johnson, Pontus Skoglund, Anthony J Onorato, Nicholas H Bergman, David Reich, Jodi A Irwin
High throughput sequencing (HTS) has been used for a number of years in the field of paleogenomics to facilitate the recovery of small DNA fragments from ancient specimens. Recently, these techniques have also been applied in forensics, where they have been used for the recovery of mitochondrial DNA sequences from samples where traditional PCR-based assays fail because of the very short length of endogenous DNA molecules. Here, we describe the biological sexing of a ~4000-year-old Egyptian mummy using shotgun sequencing and two established methods of biological sex determination (RX and RY ), by way of mitochondrial genome analysis as a means of sequence data authentication...
March 1, 2018: Genes
C Phillips, K Butler Gettings, J L King, D Ballard, M Bodner, L Borsuk, W Parson
The STR sequence template file published in 2016 as part of the considerations from the DNA Commission of the International Society for Forensic Genetics on minimal STR sequence nomenclature requirements, has been comprehensively revised and audited using the latest GRCh38 genome assembly. The list of forensic STRs characterized was expanded by including supplementary autosomal, X- and Y-chromosome microsatellites in less common use for routine DNA profiling, but some likely to be adopted in future massively parallel sequencing (MPS) STR panels...
February 21, 2018: Forensic Science International. Genetics
Hyun-Chul Park, Eu-Ree Ahn, Ju Yeon Jung, Ji-Hye Park, Jee Won Lee, Si-Keun Lim, Won Kim
DNA methylation has important biological roles, such as gene expression regulation, as well as practical applications in forensics, such as in body fluid identification and age estimation. DNA methylation often occurs in the CpG site, and methylation within the CpG islands affects various cellular functions and is related to tissue-specific identification. Several programs have been developed to identify CpG islands; however, the size, location, and number of predicted CpG islands are not identical due to different search algorithms...
February 17, 2018: Forensic Science International. Genetics
Inge Smeers, Ronny Decorte, Wim Van de Voorde, Bram Bekaert
DNA methylation is a promising biomarker for forensic age prediction. A challenge that has emerged in recent studies is the fact that prediction errors become larger with increasing age due to interindividual differences in epigenetic ageing rates. This phenomenon of non-constant variance or heteroscedasticity violates an assumption of the often used method of ordinary least squares (OLS) regression. The aim of this study was to evaluate alternative statistical methods that do take heteroscedasticity into account in order to provide more accurate, age-dependent prediction intervals...
February 9, 2018: Forensic Science International. Genetics
Angie Ambers, Jitka Votrubova, Daniel Vanek, Antti Sajantila, Bruce Budowle
Bones are a valuable source of DNA in forensic, anthropological, and archaeological investigations. There are a number of scenarios in which the only samples available for testing are highly degraded and/or skeletonized. Often it is necessary to perform more than one type of marker analysis on such samples in order to compile sufficient data for identification. Lineage markers, such as Y-STRs and mitochondrial DNA (mtDNA), represent important systems to complement autosomal DNA markers and anthropological metadata in making associations between unidentified remains and living relatives or for characterization of the remains for historical and archaeological studies...
February 23, 2018: International Journal of Legal Medicine
Leire Palencia-Madrid, Sergio Cardoso, Fernando Castro-Maestre, Igor Baroja-Careaga, Ana M Rocandio, Marian M de Pancorbo
This work presents the design, development and optimization of a screening method based on single-base extension sequencing to simultaneously analyze a panel of 52 mitochondrial SNPs. This enables to recognize the main mitochondrial haplogroups and to discriminate even between lineages from the same phylogenetic branch that diverged in different continents. The unavailability of individuals harboring infrequent variants was a limitation to optimize the panel. To overcome this, we have modified DNA by site-directed mutagenesis to create the unavailable allelic variants...
February 21, 2018: Mitochondrion
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